MetaFilter posts tagged with genome

One genome, two plants

Joe in Australia — Sun, 12 May 2013 19:00:37 -0800

Mosses Make Two Different Plants From the Same Genome, and a Single Gene Can Make the Difference

One of the most astonishing secrets in biology is this: every plant you see makes two different plants from the same genome. And, scientists recently reported, a single gene from an ancient, powerful lineage can make the difference.

Your Happy Ending

smrtsch — Tue, 12 Mar 2013 08:25:47 -0800

Allegations of flawed research techniques at an NIH-funded medical lab at Johns Hopkins get notice in a Washington Post article. Interesting piece on a scientific dispute, the accuser's loss of his job at Hopkins, and the suicide of one researcher from the lab whose analysis, published in Nature, came into question.

Breast cancer rules rewritten in 'landmark' study

Blasdelb — Mon, 05 Nov 2012 00:58:09 -0800

What we currently call breast cancer should be thought of as 10 completely separate diseases, according to an international study which has been described as a "landmark". The categories could improve treatment by tailoring drugs for a patient's exact type of breast cancer and help predict survival more accurately. The study in Nature analysed breast cancers from 2,000 women [Abstract] . It will take at least three years for the findings to be used in hospitals. The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups [Abstract] The elucidation of breast cancer subgroups and their molecular drivers requires integrated views of the genome and transcriptome from representative numbers of patients. We present an integrated analysis of copy number and gene expression in a discovery and validation set of 997 and 995 primary breast tumours, respectively, with long-term clinical follow-up. Inherited variants (copy number variants and single nucleotide polymorphisms) and acquired somatic copy number aberrations (CNAs) were associated with expression in ~40% of genes, with the landscape dominated by cis- and trans-acting CNAs. By delineating expression outlier genes driven in cis by CNAs, we identified putative cancer genes, including deletions in PPP2R2A, MTAP and MAP2K4. Unsupervised analysis of paired DNA–RNA profiles revealed novel subgroups with distinct clinical outcomes, which reproduced in the validation cohort. These include a high-risk, oestrogen-receptor-positive 11q13/14 cis-acting subgroup and a favourable prognosis subgroup devoid of CNAs. Trans-acting aberration hotspots were found to modulate subgroup-specific gene networks, including a TCR deletion-mediated adaptive immune response in the ‘CNA-devoid’ subgroup and a basal-specific chromosome 5 deletion-associated mitotic network. Our results provide a novel molecular stratification of the breast cancer population, derived from the impact of somatic CNAs on the transcriptome.

Mad scientist in your own basement?

lipsum — Wed, 17 Oct 2012 00:20:50 -0800

The Genome Compiler is an IDE for DNA projects for all you DIYbio enthusiasts. Previously. Previously.

Provirophages and transpovirons as the diverse mobilome of giant viruses

Blasdelb — Tue, 16 Oct 2012 15:55:54 -0800

Provirophages and transpovirons as the diverse mobilome of giant viruses

Abstract: A distinct class of infectious agents, the virophages¹ that infect giant viruses of the Mimiviridae family, has been recently described. Here we report the simultaneous discovery of a giant virus of Acanthamoeba polyphaga (Lentille virus) that contains an integrated genome² of a virophage (Sputnik 2), and a member of a previously unknown class of mobile genetic elements³, the transpovirons⁴. The transpovirons are linear DNA elements of ∼7 kb [kilobases]⁵ that encompass six to eight protein-coding genes, two of which are homologous⁶ to virophage genes. Fluorescence⁷ in situ hybridization⁸ showed that the free form of the transpoviron replicates within the giant virus factory and accumulates in high copy numbers inside giant virus particles, Sputnik 2 particles, and amoeba cytoplasm. Analysis of deep-sequencing data showed that the virophage and the transpoviron can integrate⁹ in nearly any place in the chromosome of the giant virus host and that, although less frequently, the transpoviron can also be linked to the virophage chromosome. In addition, integrated fragments of transpoviron DNA were detected in several giant virus and Sputnik genomes. Analysis of 19 Mimivirus strains revealed three distinct transpovirons associated with three subgroups of Mimiviruses. The virophage, the transpoviron, and the previously identified self-splicing introns¹⁰ and inteins¹¹ constitute the complex, interconnected mobilome¹² of the giant viruses and are likely to substantially contribute to interviral gene transfer.

[Full Text PDF] and two explanations in English (*#*) indicates that the article referenced is openly accessible Introduction:

Mobile genetic elements (MGEs) that are collectively referred to as the “mobilome” are key players in the genome evolution of prokaryotes (*1*) and eukaryotes (*2*, *3*) and are considered “genetic engineers” of biological innovation (*1*). MGEs can be roughly grouped into four major classes: transposable elements (TEs), plasmids, viruses, and self-splicing elements such as group I and II introns and inteins (*4*). The mobilomes of many bacteria, archaea, and unicellular eukaryotes include all of these elements in a free or integrated form. Given that viruses constitute a part of the mobilome, they are not normally considered to possess mobilomes of their own. However, some large viruses contain retrovirus sequences integrated into their genomes (*5*, *6*), whereas others, including members of the Mimiviridae family, harbor self-splicing introns and/or inteins (*7*, *8*, *9*). Furthermore, many viruses support the reproduction of satellite viruses¹ (*10*). The discovery of the Sputnik virophage in 2008 added a new twist to the existing understanding of the relationships between different mobile elements by demonstrating for the ﬁrst time that a giant virus could be infected by another, much smaller virus in a manner similar to the viral infection of cells (11). The Sputnik virophage is a small icosahedral virus (74 nm in diameter) that parasitizes on Mamavirus, a member of the Mimiviridae family (12, 13). Sputnik replicates inside Mamavirus or Mimivirus viral factories when the host giant virus is grown in amoebae such as Acanthamoeba castellanii or A. polyphaga (11). An in-depth analysis of the Sputnik proteins has suggested an evolutionary connection between this virophage and a distinct class of TEs (14). The second virophage, the Mavirus (15), was isolated as a parasite of a distinct member of the Mimiviridae family, Cafeteria roenbergensis virus (CroV) [Previously on Metafilter] (16). At least four Mavirus proteins, including the major capsid protein¹³, are homologous⁶ to proteins of Sputnik. In addition, the Mavirus genome encodes a retroviral-type integrase and a protein-primed DNA polymerase B; these proteins are homologous to the respective proteins of Maverick/polinton DNA transposons, which insert into genomes of diverse eukaryotes, suggesting an evolutionary link between the Mavirus and the polintons (15). The third complete virophage genome sequence has been identiﬁed in the metagenome of the hypersaline Organic Lake in Antarctica (*17*). This Organic Lake virophage (OLV) is thought to parasitize on phycoDNAviruses that infect green algae. The OLV genome encodes seven proteins with homologs in Sputnik (*17*), including two key proteins, the major capsid protein and the DNA-packaging ATPase, that are shared by all three virophages. Thus, the virophages apparently share a common origin, although each underwent multiple gene replacements. The virophages are likely to be common parasites of nucleocytoplasmic large DNA viruses that infect diverse eukaryotes, and show multiple evolutionary connections to other mobile elements (*18*). Here we present ﬁndings that substantially expand the complexity of the giant virus mobilome through the description of an integrated form of the virophage and of a distinct class of MGEs, the transposovirons.

Discussion:

The discovery of the Mimivirus and subsequent identiﬁcation of other giant viruses revealed unexpected complexity of viral genomes that, with over 1,000 protein-coding genes, are more complex than many parasitic and symbiotic bacteria and are comparable to the most compact genomes of free-living bacteria and archaea (*7*). The present work shows that giant viruses are associated with a commensurately complex mobilome that encompasses three of the four major classes of mobile elements, namely self-splicing elements, transposable elements or linear plasmids (transpovirons), and viruses (virophages that can form provirophages after integration into the host giant virus genome). Different components of the giant virus mobilome share homologous genes, and genomic comparisons point to DNA transfer between the mobilome components and the host virus but also within the mobilome itself. Thus, the giant virus mobilome is a network that potentially could provide routes and vehicles for gene exchange and might make substantial contributions to the shaping of mosaic viral genomes. The giant viruses and their mobilomes together are part of even more expansive, dynamic genetic networks: the amoebae with their diverse bacterial parasites and symbionts and their own viruses (30). Of special note is the transpoviron, a distinct plasmid that depends on giant viruses for its replication and spread. Substantial analogies can be found between the transpovirons and virus-associated plasmids present in bacteria and archaea. In particular, the well-studied bacteriophage P4 (also known as a “phasmid”) is a plasmid that replicates episomally in the absence of the helper bacteriophage P2 but is encapsidated into virions and thus can infect new bacterial cells in the presence of the helper (*31*, *32*). A similar replication strategy has been described for the archaeal virus plasmid pSSVx that depends on the fuselloviruses SSV1 or SSV2 and appears to have acquired genes from a fusellovirus (33). The discovery of the transpoviron shows that virus-associated plasmids exist in all three domains of cellular life. It is unlikely that the present study exhausts the diversity of the giant virus mobilome; additional virophages and transpovirons, and perhaps distinct classes of mobile elements, are likely to be discovered. Indeed, the transpoviron had not been detected until the isolation of Lentille virus from a human sample described here. Furthermore, we failed to detect closely related homologs of transpoviron genes in the available databases of environmental sequences, although close homologs of many Mimivirus and Sputnik genes were readily detectable (11). Thus, speciﬁc conditions and/or habitats could be required for accumulation of transpovirons and probably other elements comprising the giant virus mobilome. Characterization of such conditions will likely lead to the discovery of additional genetic elements associated with giant viruses and facilitate elucidation of their replication mechanisms and the relationships between different mobilome components.

Glossary of Terms Used in the Abstract, Introduction, and Discussion:

¹Virophage: A subviral agent composed of nucleic acid that depends on the co-infection of a host cell with a helper or master virus for its multiplication. When a satellite encodes the coat protein in which its nucleic acid is encapsidated it is referred to as a satellite virus. A satellite virus of mimivirus that inhibits the replication of its host has been termed a virophage. However, the usage of this term remains controversial due to the lack of fundamental differences between virophages and classical satellite viruses. ²Integrated Genome: A prophage is a phage (viral) genome inserted and integrated into the circular bacterial DNA chromosome. A prophage, also known as a temperate phage, is any virus in the lysogenic cycle; it is integrated into the host chromosome or exists as an extrachromosomal plasmid. Technically, a virus may be called a prophage only while the viral DNA remains incorporated in the host DNA. This is a latent form of a bacteriophage, in which the viral genes are incorporated into the bacterial chromosome without causing disruption of the bacterial cell. Upon detection of host cell damage, such as UV light or certain chemicals, the prophage is excised from the bacterial chromosome in a process called prophage induction. After induction, viral replication begins via the lytic cycle. In the lytic cycle, the virus commandeers the cell's reproductive machinery. The cell may fill with new viruses until it lyses or bursts, or it may release the new viruses one at a time in a reverse endocytotic process. The period from infection to lysis is termed the latent period. A virus following a lytic cycle is called a virulent virus. Prophages are important agents of horizontal gene transfer, and are considered part of the mobilome. ³Mobile genetic elements: Mobile genetic elements (MGE) are a type of DNA that can move around within the genome. They include Transposons (also called transposable elements including Retrotransposons, DNA transposons, and Insertion sequences), Plasmids, Bacteriophage elements like Mu (which integrates randomly into the genome), and Group II introns. The total of all mobile genetic elements in a genome may be referred to as the mobilome. ⁴Transpoviron: This is a new term that the authors are proposing to refer to mobile genetic elements within viruses. ⁵Kb or Kilobasepairs: A measurement of the length of a stretch of DNA equivalent to 1,000 base pairs ⁶Homology: Homologous traits of organisms are due to sharing a common ancestor, and such traits often have similar embryological origins and development. This is contrasted with analogous traits: similarities between organisms that were not present in the last common ancestor of the taxa being considered but rather evolved separately. An example of analogous traits would be the wings of bats and birds, which evolved separately but both of which evolved from the vertebrate forelimb and therefore have similar early embryology. Whether or not a trait is homologous depends on both the taxonomic and anatomical levels at which the trait is examined. For example, the bird and bat wings are homologous as forearms in tetrapods. However, they are not homologous as wings, because the organ served as a forearm (not a wing) in the last common ancestor of tetrapods. By definition, any homologous trait defines a clade—a monophyletic taxon in which all the members have the trait (or have lost it secondarily); and all non-members lack it ⁷Fluorescence: The emission of light by a substance that has absorbed light or other electromagnetic radiation. It is a form of luminescence. In most cases, the emitted light has a longer wavelength, and therefore lower energy, than the absorbed radiation. However, when the absorbed electromagnetic radiation is intense, it is possible for one electron to absorb two photons; this two-photon absorption can lead to emission of radiation having a shorter wavelength than the absorbed radiation. The emitted radiation may also be of the same wavelength as the absorbed radiation, termed "resonance fluorescence". ⁸In situ hybridization: A type of hybridization that uses a labeled complementary DNA or RNA strand (i.e., probe) to localize a specific DNA or RNA sequence in a portion or section of tissue (in situ) ⁹Viral Integration: A superpower possessed by Eukaryotic retroviruses (like HIV and Human T-lymphotropic virus) and temperate bacteriophages, where the virus integrates its genome into its host's genome and shuts off ll of its host lethal genes in order to hide - indefinitely - until conditions become better for an active infection. ¹⁰Intron: An intron is any nucleotide sequence within a gene that is removed by RNA splicing while the final mature RNA product of a gene is being generated. The term intron refers to both the DNA sequence within a gene, and the corresponding sequence in RNA transcripts. Sequences that are joined together in the final mature RNA after RNA splicing are exons. Introns are found in the genes of most organisms and many viruses, and can be located in a wide range of genes, including those that generate proteins, ribosomal RNA (rRNA), and transfer RNA (tRNA). When proteins are generated from intron-containing genes, RNA splicing takes place as part of the RNA processing pathway that follows transcription and precedes translation. The word intron is derived from the term intragenic region; i.e., a region inside a gene. Although introns are sometimes called intervening sequences, the term "intervening sequence" can refer to any of several families of internal nucleic acid sequences that are not present in the final gene product, including inteins, untranslated sequences (UTR), and nucleotides removed by RNA editing, in addition to introns. ¹¹Intein: An intein is a segment of a protein that is able to excise itself and rejoin the remaining portions (the exteins) with a peptide bond. Inteins have also been called "protein introns". ¹²Mobilome: The total of all mobile genetic elements in a genome; a play on the word Genome. ¹³Major Capsid Protein: A capsid is the protein shell of a virus. It consists of several oligomeric structural subunits made of protein called protomers. The observable 3-dimensional morphological subunits, which may or may not correspond to individual proteins, are called capsomeres. The capsid encloses the genetic material of the virus.

References from the Introduction and Discussion:

1. Frost LS, Leplae R, Summers AO, Toussaint A (2005) Mobile genetic elements: The agents of open source evolution. Nat Rev Microbiol 3(9):722–732. 2. Feschotte C, Pritham EJ (2007) DNA transposons and the evolution of eukaryotic genomes. Annu Rev Genet 41:331–368. 3. Kazazian HH, Jr. (2004) Mobile elements: Drivers of genome evolution. Science 303 (5664):1626–1632. 4. Siefert JL (2009) Defining the mobilome. Methods Mol Biol 532:13–27. 5. Sun AJ, et al. (2010) Functional evaluation of the role of reticuloendotheliosis virus long terminal repeat (LTR) integrated into the genome of a field strain of Marek’s disease virus. Virology 397(2):270–276. 6. Hertig C, Coupar BEH, Gould AR, Boyle DB (1997) Field and vaccine strains of fowlpox virus carry integrated sequences from the avian retrovirus, reticuloendotheliosis virus. Virology 235(2):367–376. 7. Raoult D, et al. (2004) The 1.2-megabase genome sequence of Mimivirus. Science 306 (5700):1344–1350. 8. Colson P, et al. (2011) Viruses with more than 1,000 genes: Mamavirus, a new Acanthamoeba polyphaga mimivirus strain, and reannotation of Mimivirus genes. Genome Biol Evol 3:737–742. 9. Van Etten JL (2003) Unusual life style of giant chlorella viruses. Annu Rev Genet 37: 153–195. 10. Simon AE, Roossinck MJ, Havelda Z (2004) Plant virus satellite and defective interfering RNAs: New paradigms for a new century. Annu Rev Phytopathol 42: 415–437. 11. La Scola B, et al. (2008) The virophage as a unique parasite of the giant mimivirus. Nature 455(7209):100–104. 12. Sun S, et al. (2010) Structural studies of the Sputnik virophage. J Virol 84(2):894–897. 13. Desnues C, Raoult D (2010) Inside the lifestyle of the virophage. Intervirology 53(5): 293–303. 14. Iyer LM, Abhiman S, Aravind L (2008) A new family of polymerases related to superfamily A DNA polymerases and T7-like DNA-dependent RNA polymerases. Biol Direct 3:39. 15. Fischer MG, Suttle CA (2011) A virophage at the origin of large DNA transposons. Science 332(6026):231–234. 16. Fischer MG, Allen MJ, Wilson WH, Suttle CA (2010) Giant virus with a remarkable complement of genes infects marine zooplankton. Proc Natl Acad Sci USA 107(45): 19508–19513. 17. Yau S, et al. (2011) Virophage control of Antarctic algal host-virus dynamics. Proc Natl Acad Sci USA 108(15):6163–6168. 18. Koonin EV, Yutin N (2010) Origin and evolution of eukaryotic large nucleo-cytoplasmic DNA viruses. Intervirology 53(5):284–292. 30. Raoult D, Boyer M (2010) Amoebae as genitors and reservoirs of giant viruses. In- tervirology 53(5):321–329. 31. Briani F, Dehò G, Forti F, Ghisotti D (2001) The plasmid status of satellite bacterio- phage P4. Plasmid 45(1):1–17. 32. Lindqvist BH, Dehò G, Calendar R (1993) Mechanisms of genome propagation and helper exploitation by satellite phage P4. Microbiol Rev 57(3):683–702. 33. Arnold HP, et al. (1999) The genetic element pSSVx of the extremely thermophilic crenarchaeon Sulfolobus is a hybrid between a plasmid and a virus. Mol Microbiol 34 (2):217–226.

Bonus:

Carl Zimmer's explanation of the debate over whether these Nucleocytoplasmic Large DNA Viruses (Giant) viruses constitute a new fourth domain of life.

Humans are less human than we thought.

Sleeper — Thu, 13 Sep 2012 03:37:03 -0800

Icky face-pooping flesh mites are only the tip of the iceberg. You've heard that your gut bacteria are necessary to help you digest, meaning not all germs are bad. Without them, we couldn't digest healthily. But stop and look at how far our interconnectedness with other forms of life goes: 1. Human DNA itself is at least 8.3% ancient viruses; without one of these viruses you could never have been born. 2. Mitochondria in human cells originated when the same type of bacteria that causes typhus disease raided one of our cellular ancestors and instead of hijacking it was pressed into service. (The same origin as chloroplasts in plants from cyanobacteria). 3. Far more of the cells in your body are non-human microorganisms than actual human cells. This relationship is not just interconnectedness. This is integration. This post was inspired by a recent post about Demodex Folliculorum. 4. There has been a reported case of a bacterium acquiring some of our DNA in the aforementioned manner, though it might have just been sample contamination. With the completion this year of both the ENCODE project (previously) and the human microbiome project, it's possible that information from one might lead to insights into the other. Life is fractal: We're complex individuals who are part of a complex society that's part of a complex species that's part of a complex biosphere. Threads in the tapestry of life. We're also tapestries ourselves: We are the universe for trillions of smaller organisms. Each of the Earth's 7 billion-plus human bodies contains about ten times more microorganism cells than human cells. Turns out, human biology is a lot like an old article in The Onion:

World's Top Scientists Ponder: What If The Whole Universe Is, Like, One Huge Atom? ....Among the revolutionary ideas expected to be raised at the historic week-long summit is the possibility that, like, our whole friggin' universe might be just one big atom in, say, some super-duper huge thing out there somewhere, or something. ...."Even weirder is, like, if we're just one big atom in a larger universe, how do we know all the little atoms don't have, you know, little universes in them, with, like, little people living on them, with little cars and little houses, and maybe even itsy-bitsy tiny-ass international symposiums on cutting-edge theoretical physics, even."

Duuude. The relationships between different organisms sharing a body is either symbiotic, commensal, parasitic, or pathogenic. Just as some microorganisms maintain symbiotic relationships with us, their hosts, we might someday find a way to be more symbiotic with the global biosphere of which we're a part. Before our host planet recognizes us as a pathogen.

Gene Map of Body's Microbes Is New Health Tool

noaccident — Wed, 13 Jun 2012 20:49:18 -0800

Gene Map of Body's Microbes Is New Health Tool

Ome

Blazecock Pileon — Sat, 05 May 2012 17:37:21 -0800

Omes have a long history and describe general interactions of biological information objects in various omes. But not all omes are real omes. Some have a problem with omes as neologisms.

Can We Influence Outcomes Together?

netbros — Thu, 05 May 2011 17:58:48 -0800

Can We Influence Outcomes Together? How can people and computers be connected so that—collectively—they act more intelligently than any individuals, groups or computers have ever done before? Can collective intelligence save the planet? An MIT Sloan Management Review studies The Collective Intelligence Genome [pdf].

master of information

kliuless — Sat, 09 Apr 2011 11:00:18 -0800

The New Biology - Eric Schadt's quest to upend molecular biology and open source it. (via)

Good News for Pregnant Needlephobes....

zarq — Wed, 08 Dec 2010 16:11:50 -0800

Invasive amniocentesis and chorionic villi sampling (CVS) tests are commonly used to determine the chromosomal, structural and genetic abnormalities in fetuses. But could they eventually become obsolete? A Chinese study has found that a complete copy of the fetal genome exists in the mother's blood, suggesting many prenatal diagnoses could potentially be performed noninvasively. Additional coverage: * Nature * Science Magazine * ScienceNews * Genome Web Daily News * New Scientist

Tragedy Transposed, The Sounds of HIV

infinite intimation — Fri, 12 Nov 2010 08:06:53 -0800

There is no question that HIV is an ugly virus in terms of human health. Each year, it infects some 2.7 million additional people and leads to some two million deaths from AIDS. But a new album manages to locate some sonic beauty deep in its genome. Sounds of HIV (Azica Records) by composer Alexandra Pajak explores the patterns of the virus's nucleotides as well as the amino acids transcribed by HIV, playing through these biologic signatures in 17 tracks. Preview samples are available to listen to on "Classics Online", and another sample is located on the SciAm blog. Some of the proceeds from the new album, which was released October 26 and is performed by the Sequence Ensemble, will go toward HIV vaccine research at the Emory Vaccine Center. Genetics- and science-inspired music are genres unto themselves, and everything from proteins to meteorite compositions have also been translated—if not always melodiously—at least tonally. Pajak took as her basic formula the National Institutes of Health's record of the retrovirus' genome and the thousands of coded letters which get transcribed by an enzyme into DNA in a cell once it's infected. But her latest work goes a step farther than simply plunking out the nucleotide-based notes (A, C, G and D, which fills in for thymine) on the keyboard. In addition to the basic base pairs, she explains, "I assigned pitches for the amino acids," which are manufactured once HIV enters a human cell. She ordered the 20 directly encoded amino acids based on their affinity for water (with arginine as the most hydrophilic and isoleucine the most hydrophobic) and gave them notes on the A minor scale based on this property. In the piece, Pajak occasionally layers amino acid and nucleotide phrases with different instruments to create musical interest, although she has kept the sequence of the notes true to the genome. Pajak decided to compose the piece in a minor scale to acknowledge the profound sadness the virus causes. Her past DNA-based pieces include a profile of the West Nile virus. She became curious about the HIV genome, especially when its complete structure was sequenced to single-nucleotide resolution in 2009, and decided to explore it "just for myself to see what it would sound like."

Venter creates spiraling coils of self-replicating DNA.

BoatMeme — Thu, 20 May 2010 10:50:37 -0800

"The ability to design and create new forms of life marks a turning-point in the history of our species and our planet." - Freeman Dyson, on the J.C. Venter Institute's creation of a cell controlled by a synthetic genome. We are now in the business of engineering life.

Sequencing of the Neandertal genome completed

Blazecock Pileon — Thu, 06 May 2010 12:40:54 -0800

Neandertals are the closest ancestral relatives to modern humans. Today, Nature published a special report on the Neandertal genome, for which a draft sequencing of three billion nucleotides has been completed. This high-throughput sequencing project shows how the genetic relationship between Neandertals and modern Europeans and Asians suggests localized interbreeding between the two species roughly 40-80,000 years ago, complicating the common "out-of-Africa" story of how modern humans originated. Additional research extends this low-coverage, first-pass sequencing with a microarray approach that uncovers specific differences between the human and Neandertal genomes.

"You Can't Patent Nature"

zarq — Wed, 31 Mar 2010 12:53:09 -0800

Followup to this post: A US District Court has ruled that Myriad Genetic's patents on breast cancer genes BRCA1 and BRCA2, which allow them to hold exclusive rights to a widely used genetic test for inherited breast and ovarian cancer susceptibility, are invalid. Genomics Law Report analyzes the ruling in two posts. The decision is likely to be challenged in a legal appeal — but if upheld, it could have huge implications for the biotechnology industry. Biotech stocks tumbled after the announcement. Fortune's Daily Brainstorm blog asks, "Is the DNA Patent Dead? GenomeBoy: After the Gold Rush Discover: Tuesday’s decision, if upheld, could have wide repercussions for the multi-billion dollar biotech industry, which is built on more than 40,000 gene patents. Already, about 20 percent of the human genes have been patented. The decision, however, is not binding on other federal courts and other judges may or may not abide by it. But it does the set the stage for years of litigation over other gene patents. Myriad Genetics plans to appeal the judgment.
AOL Daily Finance: "After a U.S. District Court ruling yesterday, women in America may soon be able to get the same access to inexpensive, verifiable gene-testing for breast cancer that women in Europe currently enjoy."

I'm sure this'll end well....

zarq — Mon, 22 Feb 2010 09:48:15 -0800

We may soon be able to clone Neanderthals. But should we? An essay from Archaeology Magazine examines the ethical, scientific and legal ramifications. (Via Heather Pringle's Time Machine blog, where essay author Zach Zorich posted a reply and elicited a response.) Background: Last year, a team of researchers led by geneticist Svante Pääbo at the Max Planck Institute announced that they had completed a draft sequence of the Neanderthal genome. The project was begun in 2006. William Saletan covered some of the same ground in Slate in 2008, as did Reason.com last year: One science fiction trope says that it is impossible for two intelligent species to evolve simultaneously on the same planet since one would inevitably out-compete the other. This may have happened on our planet. Neanderthals disappeared around the same time that modern humans began to move into their territory. New research suggests that our ancestors killed them off. Perhaps we should use modern science to resurrect Neanderthals in order to right an ancestral wrong.

More humans are alive today than had ever lived before 10,000 BC

grobstein — Tue, 19 Jan 2010 23:50:00 -0800

The human population of Earth has almost always been about 50,000. "Geneticists have long known that the ancestors of modern humans numbered as few as 10,000 at some time in the last 100,000 years." But new research indicates that that figure was not a one-time bottleneck, but rather the normal state of human affairs for at least the last million years or so. Pre-historic humans -- biologically just like us -- were just a second-rate ape species waiting to be wiped out by an environmental shock. (via)

Do they preserve scientific transparency, protect profits or both?

zarq — Wed, 13 May 2009 10:16:38 -0800

On behalf of medical organizations, universities, & individual patients, pathologists and genetics researchers, the ACLU has filed a lawsuit against Utah-based Myriad Genetics and the US Patent and Trademark Office. Myriad holds the US patents to the BRCA1 and BRCA2 genes, associated with hereditary causes of breast and ovarian cancers. Their patents guarantee the company the right to prevent anyone else from testing or studying those genes, which the ACLU says is unconstitutional and inhibits researchers from finding treatments and cures. The ACLU has posted a FAQ explaining the suit. It might be news to some that genes, gene fragments and the tools used to assess them can be patented. Here's some general info on patent eligibility and qualifications. Some question whether such patents spur or stifle research Myriad's BRCA test to measure the likelihood that someone would develop ovarian or breast cancer was in the news a couple of years ago, when a study revealed that it produces false negatives. Concerns were also raised in the EU over the patents when they were initially filed. Previously on MeFi

Jurrassic World

Brandon Blatcher — Thu, 20 Nov 2008 19:56:33 -0800

We get you real woolly mammoth, very cheap, good quality.

Personal Genome Project

thatbrunette — Mon, 20 Oct 2008 18:20:31 -0800

Volunteers from the general public working together with researchers to advance personal genomics. 10 volunteers, among them noted author and cognitive psychologist Stephen Pinker, have open sourced (so to speak) their genetic information. The belief is that current privacy issues surrounding genetic information is leading to a decline in research. With a hoped for 100,000 participants the idea is to give a boost to medical research involving the human genome. Pinker and the 9 other volunteers have posted up their medical history, and will add information such as tastes and preferences, ethnic backgrounds. Future volunteers will do the same, along with photographs, allergies- even television habits. Want to join?

Down

chuckdarwin — Fri, 08 Aug 2008 18:08:33 -0800

The Genius of Charles Darwin Warning: Dawkins haters, click away now. And, yes: eponysterical.

“There is nothing quite as enigmatic as a platypus”

Large Marge — Thu, 08 May 2008 21:09:55 -0800

It turns out if it looks like a duck it's partly a duck. A bunch of scientist got together and set about to decode the platypus genome, and guess what!?! "What we found was the genome, just like the animal, is an amazing amalgam of reptilian and mammal characteristics with quite a few unique platypus characteristics as well". “You have got these reptilian repeat patterns and these more recently evolved milk genes and independent evolution of the venom. It all points to how idiosyncratic evolution is.” “We have microRNAs that are shared with chickens and not mammals as well as ones that are shared with mammals, but not chickens.” Also, apparently, male platypi have venomous spikes on their heels that can kill dogs! For those who can't access this really really awesome Nature write up here's a really cool factoid: every sperm gets a set of all Xs or all Ys. Despite the similar designations, none of the platypus X chromosomes resembles the human, dog or mouse X. “The sex chromosomes are absolutely, completely different from all other mammals. We had not expected that”

Synthetic life is now just around the corner.

geeknik — Sat, 26 Jan 2008 12:02:22 -0800

Scientists have built the first synthetic genome by stringing together 147 pages of letters representing the building blocks of DNA.

Genome

i_am_a_Jedi — Sun, 16 Sep 2007 05:08:13 -0800

The Diploid Genome Sequence of J. Craig Venter. (Previous MeFi)

How to Sequence a Genome

McLir — Thu, 23 Aug 2007 17:16:53 -0800

How to Sequence a Genome [Flash. H/T to Jay]. Visualization of the process of genetic sequencing. Posted on the Nova website in conjunction with their show, Cracking the Code of Life, hosted by Robert Krulwich [Wiki].